Pre-requisites, installation, and execution of HPVDetector:
Pre-requisites:
1.Linux/Unix based Operating System (Ubuntu, Fedora, Red Hat, Novell Suse)
2.RAM: 6GB or more.
3.Burrows Wheeler Aligner (BWA) (minimum Ver. 0.6.*) (http://bio-bwa.sourceforge.net/)
4.Awk scripting language (generally included in Linux/Unix system) (en.wikipedia.org/wiki/AWK)
5.Yad for GUI (generally included in Linux/Unix system) (sourceforge.net/projects/yad-dialog/)
6.Picard Tools (http://broadinstitute.github.io/picard/)
Decompress the HPVDetector_v0.1.tar.gz file to a suitable location.
HPV Detector package bundle zip is composed of following files:
1.HPV Detector programme files.
2.Directory of indexed HPV reference genome.
3.Directory of indexed Human-HPV pseudo reference genome files.
4.Directory of HPV-Human Gene Annotation file.
5.In case YAD is required to be installed:
Command for RHEL/Fedora/Cent OS: sudo yum install yad
Command for Ubuntu: sudHPVDeteo apt-get install yad
6.In case BWA is required to be installed, run following commands:
wget –O bwa-0.6.2.tar.bz2 http://sourceforge.net/projects/bio-bwa/files/bwa-0.6.2.tar.bz2/download
tar -xvf bwa-0.6.2.tar.bz2
cd bwa-0.6.2/
make
7.In case Picard tool is required to be installed, run following commands:
wget -O picard-tools-1.100.zip
http://sourceforge.net/projects/picard/files/picard-tools/1.100/picard-tools-1.100.zip/download
unzip picard-tools-1.100.zip